City of Stones
by beexo
Summary: following Clary and Jace, as he trains her to become a Shadowhunter, and follows as Clary as she trains and gets her powers under control. It's a work in progress! hope you like it,
1. Chapter 1

Fan Fiction – Chapter 1: Training.

It's been a few months since the battle against Valentine…

I am currently at the institute alongside Jace, Isabelle, and Alec. Jace is helping me train to be a Shadow hunter. It's going pretty well I'd like to say, but Jace disagrees some days, especially when I am creating new runes. They tend to be too powerful. I just laugh and he gives me his famous crooked smile. It makes me melt.

It was Sunny out on a Saturday afternoon and Isabelle was helping me with my training alongside Jace. She had her long snake like golden whip out and was getting ready to attack me. Then I jumped up and yelled out "Aella!" which seemed appropriate seeing that it was a feminine name and it meant "whirlwind" which not to brag but I was fairly fast when fighting. Isabelle lurched at me vastly. But I was a tad bit faster and then Isabelle was whip less. "Dang Clary, you're getting good", Isabelle said as I helped her up. "It's my turn let me try", it was Jace. He smiled at me and then he backed up so he was about thirty feet away from me, stele in hand. "Cassile!" he yelled out. He jumped into the air and leaped forward toward me. Jace is a very good fighter, I usually lose against him. Slashing at my right side I leapt away from him and yelled out once again "Aella!" with more energy this time, my stele was shining in my hand flaming a glittery purple color. Then as I got lost in the moment all or a sudden I could feel something pricking me and then my stele was across the courtyard. Jace was on top looking down at me.

"Never let your guard down when fighting Clary", he smirked. I glared at him.

"Well you sir should know better I am not as good as you, I am a beginner!" I said with a hint of sarcasm and couldn't help but smile at him. He smiled back at me, I got lost in his liquid golden eyes. "Ahem", it was Isabelle looking at us waiting for us to come out of our reverie. Jace got up and helped me onto my feet.

"Well that went fairly well don't you think?" Jace asked. "Mhm", was my reply I was smiling at the ground thinking about the night in the green house, it seemed like a lifetime ago. But in reality it wasn't long ago it was only about a year ago. So many things had happened this past year, some were terrible, and some were great, but the one that haunted me for months was when Jace and I had thought that we were siblings only to find out that Jace and I were not, which was a relief because I am so madly in love with him. And I'm happy to say that he feels the same way about me!

The only thing that bugs me about those dark memories is when I was with Sebastian my actual brother. He hurt the thing I care about the most. Jace. He's my entire world and I'm pleased that I have him. Sebastian almost killed him and I fear that I have not seen the end of him. I haven't told Jace about the nightmares yet. They have been coming almost every night now. Not long after I found out about what Jace had gone through during the time we were separated in Idris. The description of what he went through still haunts me. I wasn't there but I felt his pain as he was telling me what happened. Those black eyes, those unending pitted black eyes still haunt me in the night. I should have known but I just couldn't figure it out. I knew there was something about Sebastian that just wasn't right. I just knew it.


	2. Chapter 2

Chapter 2: Nightmares

I remember that night. The very first night I had that nightmare. That feeling of not being able to do anything to help him I felt totally oblivious. My mind was swirling. I was screaming and yelling trying to get his attention. Trying to get his attention so that I could just let him escape and to rest for a few minutes. I was yelling so loud I don't know how they didn't hear me. I was flailing and yelling until my lungs hurt. I finally had to stop and catch my breath. "JACE!!" I screamed. "Clary, clary sweetheart. I'm right here. Its okay, it's okay". "Oh, Jace you're alright…" "Of course I'm alright" he replied confused.

"What happened?"

"Nothing" I said shyly. "It's nothing, I'm fine"

"Are you sure?" he asked his brows furrowing with worry, holding my gaze trying to figure out what's been bugging me. What had me so worried and scared. I know he doesn't believe me. But I have to keep in the blue. I don't want to bother him with these obscene nightmares that probably mean nothing. But in the back of my mind I know something is wrong. I know I need to protect him. Something is coming I can feel it in my bones, because I get the chills every time I think about it. I know something's out there.

I just don't know what…

"What are you thinking?" Jace asked me breaking me out of deep thought. "Nothing, it's not important", I replied.

* * * * *

The next few weeks have been cruel, I haven't gotten much sleep. Jace is beginning to worry. He keeps asking and looking at me trying to figure out what's happening. But no matter what I do before I go to bed. They keep returning. Something is about to go down. I keep seeing innocent people running down the streets of Idris. Fire is Blazing everywhere in different parts of the city. Screaming is filling the night air. I shiver as a chill is sent down my spine and i swirl around and see a dark figure behind me all I see are these dark eyes. I know these dark eyes. I've seen them before. Looked into them and saw something that I remember I didn't like. I know who these eyes belong to. But before I even get a word out a voice cuts me off. He puts his finger to my lips and says " You know what will happen don't you?"

I blink at his eyes. Placing his eyes and voice together...I think back and realized who's been doing this to me.

"I know who you are", I threaten.


	3. Chapter 3

Chapter 3 – Threat

"I know who you are", I threaten. I peered into his eyes. Looking for that familiar eerie shadow that haunted him and then there it was that flicker one second it was there and the next it was gone.

"I know who you are, and I'm not afraid of you!" I said sternly.

"Oh really?" he asked tauntingly.

"Yes", I replied.

"Who am I?" he asked.

One person whom I was absolutely positive of who he was.

"Sebastian!"

"Mmm hmm so you say, but yes little sister you are right. It is me Sebastian"

I glared at him and knew that I had to do something. I ripped out my stele and yelled out "Agatha", stepping back from him. Even though he was my brother he had to pay for almost killing my beloved Jace. He was going to go down!

"Ha ha ha" he laughed.

"Do you really think that you can kill me Clary?" he taunted.

"Yes. I. Do." I replied angrily knowing that I should strike but something in me wasn't letting me strike. Something was telling me to take it easy and to wait till I was sure that I was ready.

Silence…

I wasn't sure if he had left.

"Clary you're dreaming…remember?" he mocked.

I woke up and jumped right off my bed. "Oh my god!" I gasped.

I knew it was him. I knew he'd come back eventually. That was it I had to be ready, but I couldn't let Jace know what I was up to.


	4. Chapter 4

Chapter 4: Plan and Secret

I had to make a plan in order to make sure that I was prepared in case Sebastian was coming. I got out my sketchbook and started to brainstorm ideas for new runes. I knew that I was powerful that way and needed ideas for protecting Jace. There had to be a way to protect him. I just knew it.

I got to work. I tried a bunch of different ideas but it was like I was having a writer's block. I couldn't figure out the right kind of rune to make. I knew that it had to be a strong one. And I knew it would work if I could just think of the right kind of one.

Then someone knocked on my door… I shoved my sketchbook under the mattress and replied to the know

"Y-yes?" I asked.

"Clary? It's Jace" he said a tinge of worry underneath.

"Come in" I replied.

"Hey! Umm I was wondering if we could talk?" he asked coming and laying beside me on the bed.

"About what may I ask?"

"It's about the nightmares that you've been having and it's about your strange behavior that's been going on recently Clary, because honey I'm worried about you" he said sincerely stroking my cheek. I was looking down fidgeting with a loose thread on the sheet. He pulled my face up to his and stared at me for a moment that seemed like forever. I knew that I should tell him right then and there; however, the incident back in Idris had made me a stronger person and right now Jace was the one that I needed to protect so I didn't tell him. I will soon when the time is right and I have a plan.

"I'm fine Jace, there's nothing wrong with me, and you shouldn't worry because they're just nightmares maybe it's because I feel guilty for pushing you away that night in Idris after we let that angel go.. Or maybe I can't help but think of what Sebastian did to you" I said a little unsteady. He winced and looked away. I know it was a low blow to remind him of that night but I had to protect him. And I know that he didn't like to be reminded of Sebastian because Jace didn't have a chance to finish him off. I know he's worried about when he'll come back.

*** FLACH BACK! ***

"Clary, you should know that of he comes back I will finish him" Jace said angered.

"But what if he comes at you first and your unaware?" I said worried.

"Babe, don't worry. I'm a shadow hunter remember? Besides I'm a pretty damn good one too!" he smiled pulling up my face assuring me that Sebastian would never get past him unnoticed. I kissed him in desperation that Sebastian would never get to him. I needed to know that he'd be safe. He responded and I lost it. I kissed him with as much love as I had pushing myself closer to him until there was absolutely no more room in between us. He responded fiercely at first then he had to stop to catch his breath.

"Clary..." he said with concern.

"What?" I asked unsure of what he was doing.

" if he comes back you have to promise me that you'll get as far away from him as possible and that you won't come back for me, because Clary if he even tries to hurt you I'd never forgive myself if he hurt you" he said seriously looking for my confirmation.

"No, no Jace I can't leave you, I will NOT leave you! Do you hear me? I am not going to leave you, never ever and your not going to fight him alone." I said hurt that he could ever ask me to leave him if Sebastian came back.

"Clary…" he breathed in my hair and kissed it. He looked into my eyes and I knew I was crying but didn't care anymore.

"Clary… I don't care about what happens to me if he comes, but I do care about what happens to you I don't want you to risk your life against him do you understand me? Do you not understand that I love you more than anything else in my life?" he asked furious but still calm.

"Yes I do, but do you understand what I would be going through if YOU died? Do you not know what that would do to me? Jace you are asking me to run away from you if he comes back. And I can't do that I WON'T do that. Do you understand? I don't care if he brings an army with him I am and will NOT leave you" I said calmly to him. Poking his chest each time I emphasized that I WOULDN'T LEAVE him.

"Clary… I need you to be safe I can't lose you again" he said staring into my eyes then he kissed me with even more desperation. I kissed him back fiercely.

"Jace, I will NOT leave you." I said desperate that he's change his mind.

"Clary, you will leave. Promise me you will. I don't want him to find you..." he said desperately.

"Okay" I lied. Kissing him to make it out like I caved in. but I wasn't going to leave him.

I would never leave him. And I'd make sure Sebastian would get hat was coming to him if it was the last thing I had to do.

*** END OF FLASHBACK! ***

"Jace, I promised you that I'd leave if he ever came back" I said with hesitation.

"I know and I hope that you understand that I can't bare to have you in danger ever again" he said peering into my eyes.

"I know and I'll keep my promise to you, because I love you. And I would do anything for you, you know that right?" I said.

"I know" he smiled.

"But I will not leave you unprotected and vulnerable to him" I said sternly looking into his eyes smiling.

"What do you mean?" he asked confused.

"I've been planning incase he comes back" I smiled. Then I leaned over him and pulled out my sketchbook. The time was now and I had to protect him. I would protect him and I didn't care if he didn't like it or not. I would protect him if it killed me. That's how much I loved him.

"Look here..." I pointed at my rough ideas.

He peered down and I stared into his liquid golden eyes.

"I need your help and won't take no for an answer" I said shyly. Looking down at the paper.


	5. Chapter 5

Chapter 5- Haunting.

3 months later…

I felt safer there was no longer a weight on my shoulders. That weight had been lifted after I told Jace the truth about my being so secretive and distant. The nightmares had reseeded with time and I no longer had the purplish bruises under my eyes anymore. I was no longer sallow and bleached white my face was a nice ivory again my hair longer and curling wildly a flaming red, the color of poppies.

Just when I thought that Sebastian had given up on haunting me in my dreams it happened… again.

"You know you can't escape me little sister"

"Why are you doing this?" I said fists clenched at my sides. I was so over this. I was so ready to end him.

"You already know why" he smiled.

"Is it Jace? IS THAT WHAT YOU WANT??" I yelled acidic and rage carousing through my body.

"Maybe" he touched my cheek and traced the line of my jaw. I quickly slapped his hand away. "Don't touch me you freak!!" I said with as much venom as I could.

"Awe, little sis I was just kidding you're so cute when you're mad, but you know what I am going to do to your precious beloved Jace? Well I'll tell…" he smirked

"WHAT? WHAT ARE YOU GOING TO DO TO HIM?" I asked.

He moved and was out of my vision I twirled and he was suddenly behind me and had his hand tightly on my shoulders gripping hard. I tried to worm out of his grasp but it was useless. "What are you going to do to him?" I pled.

"Ahh, not yet little sis, I'll tell you in time"

"UGH! I HATE YOU, LET ME GO!!!" I screamed.

"I have become very powerful little sis, I'd watch your back if I were you… and don't worry your Jace is safe… for now. As for you? I don't know maybe I'll spare you. But I have come across a very, very powerful resource one you do not yet know about and you'll have to wait and see just how powerful I am.

I awoke and grasped the sheets and was sweating a cold sweat. My hair was stuck to my neck.

"What's wrong?" Jace asked he had woken up beside me.

"S-Sebastian h-he's back…" I whimpered. "Jace, he's accumulated new power one we do not know about yet, and he's coming for the both of us" I whimpered again almost hyperventilating. "it's going to be okay" Jace said and wrapped his arms around me trying to calm me down I inhaled slowly in and out, in and out, and inhaled his scent the scent of comfort, of soap and him. Everything about him was familiar. "I'm scared Jace, I'm scared what he's going to do". "He won't lay a hand on you Clary, I'm going to make sure he doesn't and as for me don't worry I'll be fine. I'll protect you. I promise." His liquid golden eyed bored into mine and I pressed my lips to his with the need of assurance and desperation wishing that my love for him would just make everything better and ensure his safety. "Okay" I replied and smiled while hiding my worry and trying to choke back tears that were trying to escape from me like a fox trying to get out or a hunter's trap. And then Jace wrapped his arms around me and he held me like that for the rest of the night humming the lullaby that Maryse used to sing to Alec and Isabelle when they were children. And then I was submersed into a dreamless sleep.


	6. Chapter 6

Chapter 6- Clue

I woke up and Jace was still holding me but he was asleep. I slowly crept from his grasp trying not to jostle him he needed his sleep. I got up without disrupting his sleep he looked so peaceful there.

I walked into the Institute's hallway and slowly walked around looking for someone to talk to, I knew it was early and sometimes I wished that I could talk to Hodge about certain things especially this whole nightmare business with Sebastian. Ever since I found out that it was Sebastian haunting me and it had nothing to do with my subconscious that was still rocked from the visit to Iris. I knew that there was something that had to help me. I couldn't go to Hodge… not anymore; because Hodge was never coming back he was dead. Gone.

I decided that I didn't need to wake up anyone and didn't want to bother anyone. So I made my way to the library, filled with books and interesting facts about a world that I previously just joined. I opened the door slowly hoping no one would be in there. I peeked in and found that no one was there. "Phew", I sighed.

I walked down the many aisles of books and looked for something interesting to read. I let my fingers graze the many books on the shelf. Waiting to see if anything would catch my eye… just then something caught my attention.

_ The city of stones _I looked at it. Stones? I thought. Why would that be so interesting I took it off the shelf and looked at the cover.

The book was a faded black leather and thick like it held at least a couple hundred pages. It was heavy too, at least a hundred or so years old, and was just sitting here collecting dust it was mesmerizing. I opened it and was amazed at what I saw…it was in a different language one that I couldn't really understand at all, and then I looked harder at it. The words un-blurred and they were all of a sudden English and I heard in my head what was going on while I read a voice, yes a voice telling me what was going on.

_ The city of stones is only known as the Ancient world and only a few people know of. This lost world, Clary Morgenstern you have become the chosen one. You must help defeat the coming plague; we know that you can do this. We have seen it, and you will complete this task. _

It turns out that the City of Stones was an even older city that Idris and that only like the voice said only few today know of this old city and that it kind of forgotten but there are people who can help me. But what if I didn't want to be the chosen one? What if I just want to go back to a normal teenage life and sit on the couch and eat pizza? What if I just wanted to collect rocks? And didn't want to "SAVE THE WORLD FROM EVIL!"? What then? _You must understand Clary, you cannot just walk away from this you are chosen to do this, and it is your destiny. _Okay, so what do I do? _Lucian and Amatis can help you begin but then you must talk to a person in Idris named Elezar Baggins. He knows much, much more then you're soon to be father. _Alright then let's go save the world from corruption and evil dictators I thought and left the room, book under my arm. Determined now.

I left the library and headed to find Jace. He would no doubt still be in my room sprawled all over the bed. He was such a hog when he was exhausted. I hated to wake him up but I knew I had to.

"Jace" I said poking his arm. Nothing.

Ugh come on I need you to wake up I thought furiously. Then I poked him again this time on his cheek. "JACE!" I hissed again a little louder than before.

"JACE!" I repeated. He slowly woke up with a groan. "Hmm?" he looked up at me with slight confusion. "Look, this is going to sound a little far out, but listen I heard this voice in my head when I was in the Library and he said…" I was interrupted with Jace's fingers pinning my lips together with his index finger and thumb. He took a breath and flashed his crooked smile at me. I frowned at him.

"Wait you said you heard a voice in your head?" he smiled again. "Are you okay Clary?" he felt my forehead and sighed. "You feel okay? and you're not burning up…" he trailed off. I smacked his hand away.

"Shut-up! I told you it was going to sound out there..." I said as my hand twirled in the air like a loop. "Anyways, listen Jace this is serious" I continued to tell him my story and he listened.

"So…what do you think?" I asked after I was finished. "Huh" was all he said.

"HUH? That's it HUH! You nub! Seriously tell me what you think. THIS IS SERIOUS JACE LIGHTWOOD!" I screeched with fury. He was being so cavalier about this. Sweet Mary mother of pearl. "Clary, what I mean is that I don't know what to think personally…it sounds like something dark, and magical. Maybe we should go and see Magnus about this thing that's been going on in your head". He twirled his fingers around my face as he lay beside me on the bed. "Maybe, But I'm not sure what to do…and these dreams with Sebastian are continuous and won't go away. It's maddening and I'm getting the feeling that he's still alive and won't stop until you or I are dead. I'm getting scared Jace". I trialed off and laid beside him my body facing his and he lightly traced lines on my arms up and down, up and down and so on.

"Clary, I won't let him get anywhere near you, I promise. Do you hear me? He's not gonna get you or me for that matter if that's what your worried about" I glanced up at him in shock. "IF that's what I'm worried about?" I huffed in disbelief. "IF! Are you kidding me? Jace you are my ENTIRE world and your asking IF _I'm _worried!" I was pretty sure I was a bright red but I didn't care. Jace rolled his eyes lazily. "Calm down Clary, you know I'll be okay. Don't you? We'll get everything sorted out, but for now let's go get some breakfast. I'm hungry". With that we were off to food to join Isabelle and Alec.

I huffed beside him in utter disbelief thinking about this new magical city, and all these haunting nightmares it was exhausting to think about. We arrived into the kitchen. Isabelle in a purple pajama set and a Japanese Kimono on top. Alec dressed in a woolen sweater and plaid pajamas, and his hair all miss-happened. They peered at us as we came in the kitchen.

"Hey!" Alec greeted us in a quiet still kind of tired voice.

"Hey Bro" Jace replied back and took a seat across from him. Jace had changed his name to Jace Lightwood, after our trip to Idris. Even though he is technically a Herondale, Jace didn't feel right taking that name since he never knew his actual parents. The silver box of letters and keep sakes were the only things he had that held a connection to his mother and father. But Maryse and Robert were more than willing to officially adopt Jace since he's been with them for almost eight years. They've watched him mature, grow, and finally love them over the years. I'm happy for him, and so is he I can tell.

"Alright, down to business then…" Jace started to say as I pulled out the book. Isabelle and Alec began to hover over the book and listened intently as Jace explained and I filled in the blanks. It was intriguing to watch them so enthusiastic and interested in something that _I _had discovered.


End file.
